Variant report

Variant	rs2336670
Chromosome Location	chr3:52998504-52998505
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11130331	0.85[CEU][hapmap]
rs11130332	0.81[ASN][1000 genomes]
rs11922975	0.81[CEU][hapmap];0.93[YRI][hapmap]
rs2245424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2246556	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2255107	0.85[JPT][hapmap]
rs2257216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2336669	0.90[JPT][hapmap]
rs2336672	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439434	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465101	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2564930	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2564947	0.85[JPT][hapmap]
rs2581780	0.85[JPT][hapmap]
rs2581801	0.85[JPT][hapmap]
rs2581803	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2581810	0.90[JPT][hapmap]
rs2581815	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2581816	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581819	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2581827	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710313	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2710314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710339	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2710346	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35380116	0.80[ASN][1000 genomes]
rs4515041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519686	0.90[JPT][hapmap]
rs4687687	0.81[CEU][hapmap]
rs6445550	0.90[JPT][hapmap]
rs6768844	0.90[JPT][hapmap]
rs6771610	0.80[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6792578	0.90[JPT][hapmap]
rs6795646	0.82[YRI][hapmap]
rs6799185	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs6801235	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7626551	0.82[CEU][hapmap];0.90[YRI][hapmap]
rs7648514	0.88[JPT][hapmap]
rs9311485	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9810807	0.84[YRI][hapmap]
rs9823697	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9831409	0.80[ASN][1000 genomes]
rs9846976	0.90[JPT][hapmap]
rs9860296	0.82[YRI][hapmap]
rs9865094	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9985365	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2336670	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2336670	ITIH4-AS1	cis	lung	GTEx
rs2336670	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2336670	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
2	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
3	chr3:52962400-53001600	Weak transcription	Brain Angular Gyrus	brain
4	chr3:52962400-53007000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
6	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
8	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood
9	chr3:52966400-53001600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:52969000-53008000	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:52975000-53008000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:52975200-53000600	Weak transcription	Hela-S3	cervix
13	chr3:52977600-53017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:52984000-52998800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:52984400-53006000	Weak transcription	Fetal Heart	heart
16	chr3:52984600-53003000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:52986400-53012200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:52986800-52999000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:52986800-53001600	Weak transcription	Liver	Liver
20	chr3:52986800-53006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:52987000-53002000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:52987000-53003200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:52987200-53017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:52987400-53002800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:52987400-53004600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:52987600-53003600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:52987600-53005800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:52987600-53009400	Weak transcription	Placenta	Placenta
29	chr3:52987600-53014200	Weak transcription	Fetal Thymus	thymus
30	chr3:52987600-53014200	Weak transcription	Thymus	Thymus
31	chr3:52987800-53004600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:52987800-53017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:52987800-53017000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:52988000-53003000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:52988000-53004800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:52988000-53014200	Weak transcription	Primary T cells from cord blood	blood
37	chr3:52992000-53003400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:52992000-53015800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:52992200-53005600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:52992800-53002600	Weak transcription	Ovary	ovary
41	chr3:52993800-53016800	Weak transcription	Primary B cells from cord blood	blood
42	chr3:52994000-52998600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:52994600-53001400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:52995200-53007000	Weak transcription	Right Ventricle	heart
45	chr3:52995600-52999000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:52996600-53002800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:52997200-52999800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:52997200-53008200	Weak transcription	A549	lung
49	chr3:52997400-53001800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:52998000-52998600	Strong transcription	Fetal Stomach	stomach

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